Metabolic engineering is a field where the level of a specific metabolite is quite obviously a very important thing, because that metabolite is the valuable product that one is trying to produce. If knowing the level of one metabolite is useful, it stands to reason that knowing the levels of many metabolites --- immediate precursors and products of the target metabolite, as well as other related molecules --- should be even more useful. It is perhaps surprising, then, that more metabolic engineers are not immersed in the field of metabolomics. At the very least, there is quite a natural research segue from metabolic engineering to metabolomics; beyond that, though, there is true synergy between the fields that surprisingly few have harnessed. While there are certainly instrument limitations and shortcomings of analyses in the field compared to some other more established systems-scale experimental approaches, metabolomics provides a downstream, phenotypic snapshot of the cell that can be critical to understanding metabolism and metabolic dynamics.
Here, we will discuss the intersection of metabolomics and metabolic engineering in a broad sense. While the step from metabolic engineering to metabolomics is obvious, the path back to metabolic engineering can go in many directions. We will discuss the potential for metabolomics to drive computational, semi-rational metabolic engineering (even in an age of directed evolution) by automating and expanding an intuitive process. We will consider the broader impacts of this modeling approach as we consider similar applications to understanding mammalian cell metabolism. We will also discuss the potential of metabolites as regulators, and what this means for potential future directions of metabolic engineering. Expanding on this, we will also discuss potential roles of metabolites as therapeutics, an idea with prior history and a firm grounding in biology. While past applications of metabolomics in metabolic engineering have been useful, the future potential is more broad and vast than most people realize.
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